If you corrected the distribution code, TurboTax probably doesn't see any reason to create a 5329.
The likely consequence (I don't know how likely) is that the IRS notices that you changed the distribution code on the 1099-R from the copy that they got, and so they may send you a letter asking about it.
In this case, you will respond that the distribution code was inappropriate but the administrator refused to correct it, so you had to do this workaround.
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